Development of a 44K custom oligo microarray using 454 pyrosequencing data for large scale gene expression analysis in tea plant (Camellia sinensis)

To investigate the large-scale gene expression in different tea clones, a custom oligo microarray was developed using sequences from RNA-seq for probe designing. We succeeded in developing a tea oligo microarray resource which can be successfully used to analyze gene expression in any tea clones without the need for prior sequence knowlege. A 4×44K microarray consisting of 43833 in situ synthesized 60-mer oligonucleotide probes using the 42440 unigene sequences from RNA-seq was designed. Gene expression in leaves was detected in the four tea cultivars using the microarray. Four tea plant cultivars, Longjing 43, Zhongcha 108, Zhonghuang 1 and Zhonghuang 2 were grown in the China National Germplasm Hangzhou Tea Repository (CNGHTR) at the Tea Research Institute, Chinese Academy of Agricultural Sciences (TRI, CAAS). The experiment of microarray analysis included three biological replicates for each cultivar.